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24 :     <b><font size="+3" >The SEED: an Annotation/Analysis Tool Provided by <a href="FIG.html">FIG</a></font></b>
25 :    
26 :     <br>
27 : disz 1.9 [
28 :     <a href="../index.cgi">The SEED</a> |
29 :     <a href="http://subsys.info">Subsystem Forum</a> |
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38 :     <br>
39 :     [<a href="http://www.genomesonline.org/">GOLD</a> |
40 :     <a href="CompleteSeedGenomes.html">"Complete" Genomes in SEED </a> |
41 :     <a href="http://au.expasy.org/">ExPASy</a> |
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43 :     <a href="http://img.jgi.doe.gov/">IMG</a> |
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58 :     <center>
59 :     <H1><center>TyrA Subsystem</center></H1>
60 :     <table class=ft cellspacing=10>
61 :     <tr>
62 :     <td width=20%>
63 :     Mozilla Firefox is recommended as the browser to give the best performance in accessing the links below.
64 :     <p>
65 :     <img src=./arrow1.jpg>&nbsp;<strong><a href=tyrACGTree.html>TyrA COHESION GROUP (CG) TREE</a></strong></img>
66 :     <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=TyrARep.html>Sources of Representative CG Sequences</a></p>
67 :     <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=TyrAExtended.html>TyrA CG Extended Table</a></p>
68 :     <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=../tyra_sequence.cgi?group=CG1>TyrA Trimmed Catalytic-core Sequences</a></p>
69 :     <img src=./arrow1.jpg>&nbsp;<strong><a href=TyrAPanels.html>TyrA CHARACTER-STATE SNAPSHOTS</a></strong></img>
70 :    
71 :     <p>
72 :     <img src=./arrow1.jpg>&nbsp;<strong>LINKS</strong></img>
73 :     <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=http://aropath.lanl.gov/> AroPath</a>
74 :     <p>
75 :     <img src=./arrow1.jpg>&nbsp;<strong>PUBLICATIONS</strong></img>
76 :     <p>
77 :     <img src=./arrow1.jpg>&nbsp;<strong>AUTHORS</strong> </img>
78 :     <p>
79 :     <img src=./arrow1.jpg>&nbsp;<strong>ACKNOWLEDMENTS</strong></img>
80 :    
81 :     </td>
82 :     <td width=30%>
83 :     <div style='text-align:justify;'>
84 :     &nbsp;&nbsp;&nbsp;The limitation in genome analysis is not
85 :     the availability of sequence data, but rather the interpretation of those
86 :     data. Errors in current annotations are abundant. Since new annotations
87 :     often rely upon the existing set of annotations, errors have proliferated
88 :     and continue to proliferate. The situation is sufficiently severe that in
89 :     many cases only experts familiar with particular pathways can recognize
90 :     and sort out errors. A major problem has been the untidy and erratic nomenclature
91 :     used to identify genes, <i>e.g.,</i><span style='font-style:normal'>
92 :     (i) use of the same name for different genes, (ii) use of the same name
93 :     for genes that, on the one hand, encode single-domain proteins, and, on
94 :     the other hand, genes that encode multi-domain proteins (due to gene fusion),
95 :     and (iii) use of different names in different organisms for genes encoding
96 :     the same protein. It is absolutely critical (and surely inevitable) that a
97 :     logical and consistent universal nomenclature be established.<o:p></o:p></span></p>
98 :     &nbsp;&nbsp;&nbsp;The SEED is taking the initiative that
99 :     this situation can best be addressed with a comprehensive, expert-assisted
100 :     manual effort that is undertaken with a realistically manageable subsystem
101 :     of metabolism. No matter how high the quality of an analysis is at a given
102 :     time, it will become outdated rapidly as new genomes come on line.
103 :     Therefore, our approach is to produce tools which are able to lock in the
104 :     current advances in analysis as they come, which are freely available and
105 :     interactive so that the previous work can be efficiently exploited, and
106 :     which is amenable to progressive updating and refinement via curator
107 :     approval at the SEED.<o:p></o:p></p>
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